Stereochemistry and 3D Molecules

3D structures leave many O-chem students as confused as Alice in Wonderland. But visualizing these molecules is as easy as believing seven impossible things before breakfast.

Wonderland is not for the faint of heart, what with the Mad Hatter and his invisible tea party, the slightly menacing grin of the Cheshire Cat, and the threatening Red Queen who likes to play croquet with peoples’ heads. Stereochemistry isn’t quite that bad, but it can be just as confusing at first.

In both Wonderland and organic chemistry, sometimes the first step is as easy as playing along and using your imagination. In time, the strange constructs of the micromolecular world will become as clear as the paint on the Red Queen’s roses. Which is to say, not that clear at all—but at least understandable!

The Weird and Wonderful World of Isomers

Structural or constitutional isomers have the same molecular formulae but different structures, such as these two alcohols:

It’s easy to see why those are different. Stereoisomers, however, are a little more complicated. All of the atoms have the same connectivity, but the position of each atom is slightly different when viewed in three dimensions.

Stereoisomers: Cis and Trans

The simplest stereoisomers are those on relatively flat molecules like alkenes or rings like cyclohexanes. Imagine them as the surface of a table, and ask yourself whether the functional groups or atoms in question would be seated on the same side (cis) or on opposite sides (trans).

Alice and the white rabbit are seated cis to each other at the Mad Hatter’s tea party. The CH3 groups are trans to each other on the alkene.

Cis- and trans- can also be used to show whether two functional groups are both above the plane of the molecule or if one is above and one is below, as in the case of rings like cyclohexanes (their 3D structures are actually more complicated, but the principle is the same).

All of the tea cups are cis to each other – facing up off the table – and all the table legs are cis to each other facing downward from the table. The teacups and table legs are trans to each other, however. In the cyclohexane, the CH3 molecules are cis to each other (both pointing up) and the Br is trans to both of them (it points down).

Tetrahedral Carbons: non-superimposable mirror images

This is where stereochemistry really takes a trip through the looking glass: chiral carbons.

As you probably remember from VSEPR, carbons take on a tetrahedral shape in order to keep all of the electrons as far apart as possible. If you have four different groups attached to the carbon, depending on how they are arranged, it’s actually possible to create two different configurations. These configurations will be mirror images of each other, but they will be non-superimposable – it’s impossible to put one over the other so that they are identical.

A chiral carbon with their mirror images.

Even rotated, they will never be identical.

Carbons like this are called chiral, because they don’t have an internal mirror plane or symmetry. They can have multiple stereoisomers, which will be called enantiomers.

When synthesizing molecules, it’s often difficult to control which enantiomer is the product of a reaction or to separate a racemic mixture (equal amounts of both stereoisomers). However, for many compounds, only one form is biologically active, because many receptor sites in the body are only built to accept one of the two. This is often a major hurdle in pharmaceutical development.

Left or Right Handed?

If you ever need a cheat sheet to remember what a non-superimposable mirror image looks like, just look down at your hands. If you line them up so that your thumbs are touching, you’ll see the palm of one hand and the back of the other. Flip them over so that you see both palms, and the thumbs will point to opposite sides. Your hands are chiral!

Because of this similarity, enantiomers are usually labeled either left- or right-handed. But how do you decide which is which for a particular enantiomer?

The Cahn-Ingold-Prelog rules standardize this process. It may seem strange at first, but the method does work – and it will give you your best chance of navigating wonderland.

First, assign each atom or molecule attached to the central one a number based on its molecular weight (1 for the highest, 4 for the lowest). Then point the lowest-valued one away from you. Follow the numbers 1-3, and see if this takes you clockwise or counterclockwise around the molecule.

The R- and S- enantiomers

If it’s clockwise, the molecule is right-handed, and you can label it the “R” enantiomer. If it’s counter-clockwise, it’s left-handed, and the molecule will be labeled “S” (from the Latin word for “left:” sinister).

Stereochemistry may be a mystical place full of strange structures and even stranger rules, but with a little practice, you’ll find your way out of the o-chem rabbit hole – as long as you have your hands to guide you!

For more details and examples on this process, watch this lecture around minute 23. The lecture also covers Fisher projections, another way of representing molecules in 3D.